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feat: add example ebolavirus mutation pattern configs #456

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5 changes: 4 additions & 1 deletion data/nextstrain/orthoebolavirus/bdbv/CHANGELOG.md
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@@ -1,3 +1,7 @@
## Unreleased

- Add mutationPatterns config for ADAR-mediated A-to-I editing detection (A>G and T>C substitution type filtering)

## 2026-05-22T16:04:17Z

- adjust QC param settings to reudce private mutation threshold (outbreak genomes should be very similar)
Expand All @@ -10,7 +14,6 @@
- add GP_003:367 to known stop codons
- Include 2026 genomes


## 2026-05-15T16:16:45Z

Initial release of this dataset.
951 changes: 951 additions & 0 deletions data/nextstrain/orthoebolavirus/bdbv/examples.fasta
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49 changes: 48 additions & 1 deletion data/nextstrain/orthoebolavirus/bdbv/pathogen.json
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Expand Up @@ -29,6 +29,48 @@
"reference": "reference.fasta"
},
"defaultCds": "GP",
"mutationPatterns": {
"patterns": [
{
"id": "adar",
"name": "ADAR-like RNA editing",
"description": "ADAR-mediated A-to-I editing (observed as A>G and complementary T>C)",
"events": [
{
"type": "nucSubstitution",
"ref": ["A"],
"qry": ["G"]
},
{
"type": "nucSubstitution",
"ref": ["T"],
"qry": ["C"]
}
],
"cluster": {
"windowSize": 50,
"cutoff": 3
}
},
{
"id": "apobec",
"name": "APOBEC-like cytosine deamination",
"description": "APOBEC-like cytosine deamination (observed as G>A)",
"events": [
{
"type": "nucSubstitution",
"ref": ["G"],
"qry": ["A"],
"motifs": ["[CT]G[ACT]"]
}
],
"cluster": {
"windowSize": 50,
"cutoff": 3
}
}
]
},
"qc": {
"frameShifts": {
"enabled": true,
Expand Down Expand Up @@ -60,7 +102,12 @@
},
"stopCodons": {
"enabled": true,
"ignoredStopCodons": [{"cdsName": "GP_003", "codon": 366}],
"ignoredStopCodons": [
{
"cdsName": "GP_003",
"codon": 366
}
],
"scoreWeight": 20
}
},
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4 changes: 4 additions & 0 deletions data/nextstrain/orthoebolavirus/ebov/CHANGELOG.md
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## Unreleased

- Add mutationPatterns config for ADAR editing and APOBEC-like CpG deamination detection

## 2026-04-14T11:55:23Z

- Align `pathogen.json` metadata with the current Nextclade schema layout.
Expand Down
37 changes: 33 additions & 4 deletions data/nextstrain/orthoebolavirus/ebov/pathogen.json
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Expand Up @@ -27,11 +27,41 @@
"readme": "README.md",
"reference": "reference.fasta"
},
"mutationPatterns": {
"patterns": [
{
"id": "rna_editing",
"name": "RNA editing signatures",
"description": "ADAR editing (A>G, T>C) and APOBEC-like deamination (C>T in CpG context)",
"events": [
{
"type": "nucSubstitution",
"ref": ["A"],
"qry": ["G"]
},
{
"type": "nucSubstitution",
"ref": ["T"],
"qry": ["C"]
},
{
"type": "nucSubstitution",
"ref": ["C"],
"qry": ["T"],
"motifs": ["[ACGT]CG"]
}
],
"cluster": {
"windowSize": 100,
"cutoff": 5
}
}
]
},
"qc": {
"frameShifts": {
"enabled": true,
"ignoredFrameShifts": [
],
"ignoredFrameShifts": [],
"scoreWeight": 50
},
"missingData": {
Expand Down Expand Up @@ -59,8 +89,7 @@
},
"stopCodons": {
"enabled": true,
"ignoredStopCodons": [
],
"ignoredStopCodons": [],
"scoreWeight": 50
}
},
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4 changes: 4 additions & 0 deletions data/nextstrain/orthoebolavirus/sudv/CHANGELOG.md
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## Unreleased

- Add mutationPatterns config for ADAR editing detection

## 2026-04-14T11:55:23Z

- Align `pathogen.json` metadata with the current Nextclade schema layout.
Expand Down
31 changes: 27 additions & 4 deletions data/nextstrain/orthoebolavirus/sudv/pathogen.json
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Expand Up @@ -26,11 +26,35 @@
"readme": "README.md",
"reference": "reference.fasta"
},
"mutationPatterns": {
"patterns": [
{
"id": "adar",
"name": "ADAR-like RNA editing",
"description": "ADAR-mediated A-to-I editing",
"events": [
{
"type": "nucSubstitution",
"ref": ["A"],
"qry": ["G"]
},
{
"type": "nucSubstitution",
"ref": ["T"],
"qry": ["C"]
}
],
"cluster": {
"windowSize": 80,
"cutoff": 4
}
}
]
},
"qc": {
"frameShifts": {
"enabled": true,
"ignoredFrameShifts": [
],
"ignoredFrameShifts": [],
"scoreWeight": 20
},
"missingData": {
Expand Down Expand Up @@ -58,8 +82,7 @@
},
"stopCodons": {
"enabled": true,
"ignoredStopCodons": [
],
"ignoredStopCodons": [],
"scoreWeight": 20
}
},
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30 changes: 24 additions & 6 deletions data_output/index.json
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Expand Up @@ -2233,6 +2233,13 @@
]
},
"versions": [
{
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
}
},
{
"updatedAt": "2026-04-14T11:55:23Z",
"tag": "2026-04-14--11-55-23Z",
Expand All @@ -2251,8 +2258,7 @@
}
],
"version": {
"updatedAt": "2026-04-14T11:55:23Z",
"tag": "2026-04-14--11-55-23Z",
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
Expand Down Expand Up @@ -2288,6 +2294,13 @@
]
},
"versions": [
{
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
}
},
{
"updatedAt": "2026-04-14T11:55:23Z",
"tag": "2026-04-14--11-55-23Z",
Expand All @@ -2306,8 +2319,7 @@
}
],
"version": {
"updatedAt": "2026-04-14T11:55:23Z",
"tag": "2026-04-14--11-55-23Z",
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
Expand Down Expand Up @@ -2348,6 +2360,13 @@
]
},
"versions": [
{
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
}
},
{
"updatedAt": "2026-05-22T16:04:17Z",
"tag": "2026-05-22--16-04-17Z",
Expand All @@ -2374,8 +2393,7 @@
}
],
"version": {
"updatedAt": "2026-05-22T16:04:17Z",
"tag": "2026-05-22--16-04-17Z",
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
Expand Down
19 changes: 19 additions & 0 deletions data_output/nextstrain/orthoebolavirus/bdbv/unreleased/CHANGELOG.md
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@@ -0,0 +1,19 @@
## Unreleased

- Add mutationPatterns config for ADAR-mediated A-to-I editing detection (A>G and T>C substitution type filtering)

## 2026-05-22T16:04:17Z

- adjust QC param settings to reudce private mutation threshold (outbreak genomes should be very similar)
- add SNP cluster QC rule to trigger on stretches of high private mutation density
- update tree

## 2026-05-18T20:09:34Z

- Add outbreak annotation
- add GP_003:367 to known stop codons
- Include 2026 genomes

## 2026-05-15T16:16:45Z

Initial release of this dataset.
15 changes: 15 additions & 0 deletions data_output/nextstrain/orthoebolavirus/bdbv/unreleased/README.md
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# Nextclade dataset for Bundibugyo virus (Orthoebolavirus bundibugyoense)

| Key | Value |
| ---------------------- | ------------------------------------------------------------------------------- |
| authors | [Richard Neher](https://neherlab.org) |
| data source | Genbank |
| nextclade dataset path | nextstrain/orthoebolavirus/bdbv |
| annotation | [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373.1) |

This Nextclade dataset for Bundibugyo virus [(Orthoebolavirus bundibugyoense)](https://ictv.global/report/chapter/filoviridae/filoviridae/orthoebolavirus) aligns to the reference sequence [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373) and translates major CDS. It scores the sequence with respect to unexpected frameshifts or stop codons, missing sequence (in form of `NNN`s) and mixed bases.

Data from the 2026 outbreak were generously shared by the groups of Prof. Placide Mbala-Kingebeni (INRB, DRC) and Dr Isaac Ssewanyana (CPHL, Uganda) to facilitate the public health response and containment of the virus. These data are described in a post on [Virological.org](https://virological.org/t/initial-genomes-from-may-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo-and-uganda/1032) and were deposited in Pathoplexus under [Restricted Data-Use terms](https://pathoplexus.org/about/terms-of-use/restricted-data). Please consult the authors and the [data-use terms](https://pathoplexus.org/about/terms-of-use/restricted-data) before using these sequences.



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